liana_tensor_c2c error

[estherwon]

Hello,

Thankyou for your work on this package. I have been trying to run tensor decomposition on my data after successfully running the liana_bysample. But when I try to run liana_tensor_c2c it has been giving me error related to setup.py as shown below. I tried to update setup.py but it did not work. I converted all my dataset(seurat objects) to SingleCellExperiment object before using this package. I am not sure if this error is related to setting up the conda environment, I also tried to update conda but it did not work either. Please let me know if you have any suggestions or solutions on this issue. I really appreciate your help. Thankyou.

Collecting h5py>=3 (from anndata->anndatari==1.0.6) Using cached h5py-3.11.0-cp38-cp38-macos×_10_9_x86_64.whl.metadata (2.5 kB) Collecting natsort (from anndata->anndatari=-1.0.6) Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting dunamai (from get_version->anndata2ri==1.0.6) Using cached dunamai-1.21.2-py3-none-any.whl.metadata (10 kB) Collecting get-annotations (from scanpy->cell2cell==0.6.8) Using cached get_annotations-0.1.2-py3-none-any.whl.metadata (3.3 kB) Collecting joblib (from scanpy->cell2cell==0.6.8) Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB) INFO: pip is looking at multiple versions of scany to determine which version is compatible with other requir Collecting scapy (from cell2cell==0.6.8) Using cached scanpy-1.9.7-py3-none-any.whl.metadata (6.0 kB) Using cached scanpy-1.9.6-py3-none-any.whl.metadata (6.0 kB) Collecting numba>=0.41.0 (from scanpy->cell2cell==0.6.8) Using cached numba-0.58.1-cp38-cp38-macosx_10_9_x86_64.whl.metadata (2.7 kB) Collecting patsy (from scanpy->cell2cell==0.6.8) Using cached patsy-0.5.6-py2.py3-none-any.whl.metadata (3.5 kB) Collecting session-info (from scanpy->cel12cell==0.6.8) Using cached session_info-1.0.0.tar.gz (24 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' error: subprocess-exited-with-error × python setup.py egg_info did not run successfully. I exit code: 1 L> [1 lines of output] ERROR: Can not execute setup.py since setuptools is not available in the build environment. [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. L> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details. Error in setupBasiliskEnvenvpath, packages = .getPackages(en), channels = •getChannels(env), failed to install additional packages via pip

[dbdimitrov]

Hi @estherwon,

This seems to be a recurring issue when trying to install the automatically setup environment by liana. I will try to resolve it, in the meantime, you could check setting up the environment as done here: https://github.com/saezlab/ccc_protocols/tree/main/env_setup

Honestly, I recommend following those tutorials also :)

Best wishes, Daniel